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Nomenclature of Organic Chemistry. IUPAC Recommendations and Preferred Names 2013

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Nomenclature of Organic Chemistry. IUPAC Recommendations and Preferred Names 2013 International Union of Pure and Applied Chemistry Division VIII Chemical Nomenclature and Structure Representation Division Nomenclature of Organic Chemistry. IUPAC Recommendations and Preferred Names 2013. Prepared for publication by Henri A. Favre and Warren H. Powell, Royal Society of Chemistry, ISBN 978-0-85404-182-4 Chapter P-9 SPECIFICATION OF CONFIGURATION AND CONFORMATION P-90 Introduction P-91 Stereoisomer graphical representation and naming P-92 The Cahn-Ingold-Prelog (CIP) priority system and the Sequence Rules P-93 Configuration specification P-94 Conformation and conformational stereodescriptors P-90 INTRODUCTION This Chapter is concerned only with the main principles for specification of configuration and conformation of organic compounds. The structure of an organic compound is systematically indicated by one or more affixes added to a name that does not itself prescribe stereochemical configuration or conformation; such affixes are generally called ‘stereodescriptors’. Thus, stereoisomers, such as enantiomers, have names that differ only in the stereodescriptors used. In contrast, ‘cis/trans’ isomers may have different names because of different stereodescriptors or names differing in the type of nomenclature. Also, certain retained names imply their own stereochemical description, for example, maleic acid, cholesterol, and other natural products described in Chapter P-10. In order to arrive at an unambiguous description of stereoisomers, Cahn, Ingold, and Prelog (refs. 34, 35) recommended an order of seniority for the ligands (atoms and groups) attached to carbon and other atoms, which is commonly called the ‘CIP priority system’. The priority is established by the application of ‘Sequence Rules’. These rules are discussed in P-92. Their application is then described for stereogenic units, mainly for the most usual compounds encountered in organic chemistry. Synthetic compounds are discussed in P-93 and Natural Products in Chapter P-10. When different stereodescriptors are recommended to describe cis and trans isomers, diastereoisomers, and enantiomers, one of them is recommended as a preferred stereodescriptor. This preferred stereodescriptor is used to generate a preferred IUPAC name. Obviously, in general nomenclature, any appropriate descriptor can be used. Example: (2Z)-but-2-ene (PIN) cis-but-2-ene P-91 STEREOISOMER GRAPHICAL REPRESENTATION AND NAMING P-91.1 Stereoisomer graphical representation P-91.2 Stereodescriptors P-91.3 Naming of stereoisomers P-91.1 STEREOISOMER GRAPHICAL REPRESENTATION Structural diagrams which depict configurations must be prepared with extra care. Recommendations were made in 1996 to achieve that goal (ref. 37). A new set of recommendations is now proposed in the document entitled ‘Graphical representation of stereochemical configuration, IUPAC Recommendations 2006’ (ref. 38). In general, plain lines depict bonds approximately in the plane of the drawing. Bonds to atoms above the plane are shown by a solid wedge (starting from an atom in the plane of the drawing at the narrow end of the wedge); bonds to atoms below the plane are shown by a hashed wedge interpreted in a sense similar to the solid wedge (starting from an atom in the plane of the drawing at the narrow end of the wedge). If the configuration is unknown, this can be indicated explicitly by a wavy line of constant amplitude . These bonds are used in this book, with exceptions in the field of natural products clearly indicated in Chapter P-10 for carbohydrates. In this Chapter, a single graphical representation depicts the absolute configuration of a chiral molecule. P-91.2 STERODESCRIPTORS The configuration of an organic compound is systematically indicated by one or more affixes added to a name that does not itself prescribe configuration; such affixes are called ‘stereodescriptors’. P-91.2.1 Recommended stereodescriptors P-91.2.2 Omission of stereodescriptors P-91.2.1 Recommended stereodescriptors Stereodescriptors are divided into two types: P-91.2.1.1 Cahn-Ingold-Prelog (CIP) stereodescriptors P-91.2.1.2 Other acceptable stereodescriptors P-91.2.1.1 Cahn-Ingold-Prelog (CIP) stereodescriptors Some stereodescriptors described in the Cahn-Ingold-Prelog (CIP) priority system, called ‘CIP stereodescriptors’, are recommended to specify the configuration of organic compounds, as described and exemplified in this Chapter and applied in Chapters P-1 through P-8, and in the nomenclature of natural products in Chapter P-10. The following stereodescriptors are used as preferred stereodescriptors (see P-92.1.2): (a) ‘R’ and ‘S’, to designate the absolute configuration of tetracoordinate (quadriligant) chirality centers; (b) ‘r’ and ‘s’, to designate the absolute configuration of pseudoasymmetric centers; (c) ‘M’ and ‘P’, to specify the absolute configuration of an axial or planar entity using the helicity rule; (d) ‘m’ and ‘p’, to specify the absolute configuration of a pseudoasymmetric entity using the helicity rule; (e) ‘seqCis’ and ‘seqTrans’, to describe the configuration of enantiomorphic double bonds; To specify the relative configuration the descriptor ‘rel’ associated with ‘R’ or ‘S’ is preferred to the stereodescriptors ‘R*’ or ‘S*’. Racemates are described by the descriptor ‘rac’ which is preferred to ‘RS’ or ‘SR’ stereodescriptors. The following stereodescriptors are recommended for general nomenclature: ‘Ra’ and ‘Sa’ to specify the configuration of molecular entities possessing axial chirality; ‘Rp’ and ‘Sp’, to specify the configuration of molecular entities possessing planar chirality; ‘ra’ and ‘sa’, to specify the configuration of pseudoasymmetric stereogenic axes; ‘rp’ and ‘sp’, to specify the configuration of pseudoasymmetric stereogenic planes. Capitalized CIP stereodescriptors are variant on reflection in a mirror (i.e. ‘R’ becomes ‘S’ and ‘S’ becomes ‘R’); lower- case CIP stereodescriptors are invariant on reflection in a mirror (i.e. ‘r’ remains ‘r’ and ‘s’ remains ‘s’). They are written in italics to indicate that they are not involved in the primary stage of alphanumerical order (see P-16.6). P-91.2.1.2 Other acceptable stereodescriptors Non Cahn-Ingold-Prelog (CIP) stereodescriptors are divided into two categories: P-91.2.1.2.1 Stereodescriptors used in substitutive nomenclature; P-91.2.1.2.2 Stereodescriptors used in the nomenclature of natural products (see Chapter P-10). P-91.2.1.2.1 Stereodescriptors used in substitutive nomenclature Stereodescriptors used in systematic substitutive names to specify the configuration of preferred IUPAC names and in general nomenclature; some stereodescriptors are recommended in general nomenclature only: (a) Stereodescriptors used in preferred IUPAC names (i) ‘E’ and ‘Z’ to describe the configuration of diastereomorphic alkenes R1R2C=CR3R4 (R1 ≠ R2, R3 ≠ R4 and neither 1 2 3 4 1 2 3 4 1 2 R nor R need be different from R or R ), cumulenes R R C=[C=]nCR R , systems for example, R R C=NOH and HON=C{[CH2]n}2C=NOH. The group of highest CIP priority attached to one of the terminal doubly bonded atoms of the alkene, oxime, etc., or cumulene (i.e. R1 or R2) is compared with the group of highest precedence attached to the other (i.e. R3 or R4). The stereoisomer is designated as ‘Z’ (zusammen = together) if the groups lie on the same side of a reference plane passing through the double bond and perpendicular to the plane containing the bonds linking the groups to the double bond atoms; the other isomer is designated ‘E’ (entgegen = opposite). The descriptors may be applied to structures with a fractional bond order between one or two; and to double bonds involving elements other than carbon. (ii) ‘A’ and ‘C’ to describe the absolute configuration of pentacoordinate (pentaligant, as in a trigonal bipyramid or square pyramid) and hexacoordinate (hexaligant, as in an octahedron) stereogenic centers. (b) The following stereodescriptors are recommended for general nomenclature: (i) ‘cis’, ‘trans’ and ‘r’, ‘c’, ‘t’ are used to specify the configuration of diastereomorphic double bonds (see P-93.4.2.1.1) and the relative configuration of alicyclic compounds (see P-93.5.1.3), respectively; (ii) ‘endo’, ‘exo’, ‘syn’, and ‘anti’ are used to specify the relative configuration of some von Baeyer ring systems (see P-93.5.2.2.1). In preferred IUPAC names, stereodescriptors, preceded by a locant, must be cited to specify each stereogenic unit, as illustrated in P-91.3. When the configuration is not known or must remain unspecified for lack of configurational homogeneity, the italicized symbol ‘ξ’ or ‘Ξ’ is used, preceded by the required locant (see P-91.3). The symbol ‘ξ’ (small Greek letter ‘xi’) replaces noncapitalized CIP stereodescriptors such as ‘r’, ‘s’, ‘m’, ‘p’. The symbol ‘Ξ’ (capital Greek letter ‘xi’) replaces capitalized CIP stereodescriptors such as ‘R’, ‘S’, ‘M’, ‘P’, ‘E’, ‘Z’, ‘seqCis’, and ‘seqTrans’. P-91.2.1.2.2 Stereodescriptors used in the nomenclature of natural products (see Chapter P-10): (i) The descriptors ‘D’ and ‘L’ are used to describe the configuration of carbohydrates (ref. 27 and P-102), amino acids and peptides (ref. 18 and P-103), and cyclitols (ref. 39 and P-104); (ii) The descriptors ‘erythro’ and ‘threo’ are used in the systematic nomenclature of carbohydrates, along with descriptors such as ‘arabino’ and ‘gluco’ (see ref. 27 and P-102); (iii) The stereodescriptors ‘α’, ‘β’ are used in the nomenclature of natural products to describe the absolute configuration of alkaloids, terpenes and terpenoids, steroids, and other compounds as described in P-101; (iv) The stereodescriptors ‘cis’, ‘trans’ and ‘all-E’ and ‘all-trans’ are used in the nomenclature of carotenoids and similar compounds (see ref. 40 and P-101.6); (v) The descriptor ‘meso’ is used in the nomenclature of carbohydrates to designate compounds such as alditols and aldaric acids that are symmetrical and thus optically inactive (see P-102.5.6.5.2; P-102.5.6.6.5); (vi) The stereodescriptor ‘ambo’ describes the formation of diastereoisomers by reaction at a nonstereogenic center of a chiral molecule or the reaction of a chiral compound with a racemic compound which will not normally give a 50:50 mixture.
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